Figure it with the blank assembled like you're going to be fishing with the rod. You could put the stripping guide on the first ferrule if you want. What I like to do is grip the blank where I would if I was fishing it then act like I'm reaching up to grab the line hanging from the first guide (stripping guide). The highest spot you can comfortably reach is a good place for the stripping guide.

It will likely be about where it is on the chart, but that should let you know if you should put it on the top of the first section or the ferrule of the second.
If you find you want it significantly lower than the chart indicates you'll want to re-figure the guide spacing, but that's part of the purpose of making your own rod, making it for you. No sense stretching to grab the line if you can make it comfortable.